Viewing profile — Gethsemane

For most DNA it now sits at ~Q20 (1%) which is a big improvement - there was also some hacky stuff like HERRO and duplex sequencing which improved it substantially. For routine gen…

Fastest/cheapest sequencing based method would likely be to collect samples in DNA preserving agent (zymo DNA shield is decent for this), then have an automated platform for extrac…

Have you written about your experience anywhere? It would be interesting to see how you approached the research sector as a layperson. Are there any plans to move to in vivo? Best …

With AIs as teachers, I disagree. But with AIs assisting routine grading, filling in the university's assessment_framework_draft_v3_final_FINAL.docx, and otherwise freeing up time …

Very nice! I also like working from pandoc where possible - being able to split the output into a latex/typst file as well as a docx is very handy, especially when working with col…

Ultimately you're not going to find a service that can guarantee privacy, but your best bet might be to extract DNA at home (though tricky without a centrifuge etc...) and submit i…

It's very context-dependent - the seqera rewrites so far seem to be pretty reliable, most of the work was spent merging the functions of multiple data QC tools into a single progra…

I somewhat agree, in that most of these life science adjacent demos are essentially "find good drug targets for $DISEASE", which mostly overfit to existing, well-classified drugs a…

It's also all too easy to arbitrarily label something as "bureaucratic" and demand that it gets razed and rebuilt. I'm sure Palantir has some level of bureaucracy internally with a…

A highlight of my time in Turkey was the cats - thank you for your efforts! Antalya had a lot of cat hotels in the park and most looked very healthy.

If I was less lazy I could probably find this answer online, but how do you find the battery life these days? I'd love to make the switch, but that's the only thing holding me back…

I'd love to see some benchmarks for this on some common genomic formats (fa, fq, sam, vcf). Will be doubly interesting to see its applicability to nanopore data - lots of useful da…

Unfortunately, when you write a program that doesn't wrap output FASTAs, you have a bunch of people telling you off because SOME programs (cough bioperl cough) have hard limits on …

I really want to like typer, and frequently go down the rabbit hole of rewriting all my argparse into typer, but I keep getting put off by it's high import cost and that developmen…

Agreed, there’s been some interesting developments in this space recently (e.g. AgroNT). Very excited for it, particularly as genome sequencing gets cheaper and cheaper! I’d pitch …

Something I found useful is that you can create a much more minimal pandoc template for typst than for latex. Obviously if familiar with latex it probably won't be an issue, but wh…

I've similarly found the combination of pandoc + typst to be quite exciting. I've found it particularly useful for typesetting academic papers - I'm quite averse to word in general…

I am a fan of the colour scheme they selected in figure 2 - very relevant. https://pubs.rsc.org/image/article/2024/na/d4na00601a/d4na00...

As an example of a more informative map of income/deprivation, I recently encountered the Scottish Index of Multiple Deprivation website ( https://simd.scot ). Only applicable to S…

50% CPU usage on the home page, and the firefox inspect tool crashes before it can open! The content itself doesn't load either - just a large blue box

It is a shame. Twitter used to be quite a popular platform for (useful and interesting) networking in academia, but after it began to fall apart everyone started looking for altern…

Sounds like your laptop is wholly out of date, you need to buy the next generation of laptops on Amazon that can handle the modern SEO load. I recommend the: LEEZWOO 15.6" Laptop -…

I agree that it's perhaps not the most robust choice, but at least for my field (bioinformatics) it's a good balance between accessibility and performance. That being said, in most…

Shiny is an R package that is quite popular for building data analysis web tools, I suppose this would be a useful extension for it! Despite R tending to give people 'the ick' it r…